Structure of PDB 5qco Chain B Binding Site BS01

Receptor Information
>5qco Chain B (length=377) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSA
CHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDE4A
InChIInChI=1S/C35H43N3O4/c1-23(2)26-9-7-10-29(19-26)35(12-13-35)37-22-33(40)32-17-25-8-6-11-31(16-25)42-15-5-4-14-36-30-20-27(24(3)39)18-28(21-30)34(41)38-32/h6-11,16,18-21,23,32-33,36-37,40H,4-5,12-15,17,22H2,1-3H3,(H,38,41)/t32-,33+/m0/s1
InChIKeyLUJWXMKDHHFLOK-JHOUSYSJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)c1cccc(c1)C2(CC2)NCC(C3Cc4cccc(c4)OCCCCNc5cc(cc(c5)C(=O)C)C(=O)N3)O
CACTVS 3.385CC(C)c1cccc(c1)C2(CC2)NC[C@@H](O)[C@@H]3Cc4cccc(OCCCCNc5cc(cc(c5)C(=O)N3)C(C)=O)c4
CACTVS 3.385CC(C)c1cccc(c1)C2(CC2)NC[CH](O)[CH]3Cc4cccc(OCCCCNc5cc(cc(c5)C(=O)N3)C(C)=O)c4
OpenEye OEToolkits 2.0.6CC(C)c1cccc(c1)C2(CC2)NC[C@H]([C@@H]3Cc4cccc(c4)OCCCCNc5cc(cc(c5)C(=O)C)C(=O)N3)O
ACDLabs 12.01C2(Cc3cc(OCCCCNc1cc(cc(c1)C(C)=O)C(N2)=O)ccc3)C(CNC4(CC4)c5cc(ccc5)C(C)C)O
FormulaC35 H43 N3 O4
Name(4S)-19-acetyl-4-[(1R)-1-hydroxy-2-({1-[3-(propan-2-yl)phenyl]cyclopropyl}amino)ethyl]-11-oxa-3,16-diazatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one
ChEMBL
DrugBank
ZINC
PDB chain5qco Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5qco D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Q12 L30 D32 G34 P70 Y71 T72 F108 W115 I226 D228 G230 T232
Binding residue
(residue number reindexed from 1)		Q15 L33 D35 G37 P73 Y74 T75 F111 W118 I218 D220 G222 T224
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 D220 T223
Enzyme Commision number 3.4.23.46: memapsin 2.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5qco, PDBe:5qco, PDBj:5qco
PDBsum5qco
PubMed31974851
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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